Merge pull request #13 from spapa013/main

reorganize api.config, add api.schemas, change how base imports api

python/microns-materialization-api/microns_materialization_api/__init__.py

@@ -10,4 +10,4 @@
     )
 )
 
-check_latest_version_from_github = version_utils.latest_github_version_checker(owner='cajal', repo='microns-materialization')
+check_latest_version_from_github = version_utils.latest_github_version_checker(owner='cajal', repo='microns-materialization')

python/microns-materialization-api/microns_materialization_api/config/__init__.py

@@ -1,82 +1,23 @@
 """
 Configuration package/module for microns-materialization.
 """
-
-import inspect
-import traceback
-from enum import Enum
+import datajoint.datajoint_plus as djp
+from microns_utils.config_utils import SchemaConfig
 from . import adapters
 from . import externals
-from . import bases
-try:
-    import datajoint as dj
-except:
-    traceback.print_exc()
-    raise ImportError('DataJoint package not found.')
-from microns_utils import config_utils
-
-
-config_utils.enable_datajoint_flags()
-
-
-def register_externals(schema_name:str):
-    """
-    Registers the external stores for a schema_name in this module.
-    """
-    external_stores = config_mapping[SCHEMAS(schema_name)]["externals"]
-
-    if external_stores is not None:
-        config_utils.register_externals(external_stores)
-
-
-def register_adapters(schema_name:str, context=None):
-    """
-    Imports the adapters for a schema_name into the global namespace.
-    """
-    adapter_objects = config_mapping[SCHEMAS(schema_name)]["adapters"]
-
-    if adapter_objects is not None:
-        config_utils.register_adapters(adapter_objects, context=context)
-
-
-def register_bases(schema_name:str, module):
-    """
-    Maps base classes to DataJoint tables.
-    """
-    bases = config_mapping[SCHEMAS(schema_name)]["bases"]
-
-    if bases is not None:
-        for base in bases:
-            config_utils.register_bases(base, module)
-        return module
-
-
-def create_vm(schema_name:str):
-    """
-    Creates a virtual module after registering the external stores, adapter objects, DatajointPlus and base classes.
-    """
-    schema = SCHEMAS(schema_name)
-    vm = config_utils._create_vm(schema.value, external_stores=config_mapping[schema]["externals"], adapter_objects=config_mapping[schema]["adapters"])
-    config_utils.add_datajoint_plus(vm)
-    register_bases(schema_name, vm)
-    return vm
-
-
-class SCHEMAS(Enum):
-    H01_MATERIALIZATION = "microns_h01_materialization"
-    MINNIE65_MATERIALIZATION = "microns_minnie65_materialization"
-
 
-config_mapping = {
-    SCHEMAS.H01_MATERIALIZATION: {
-        "externals": externals.h01_materialization,
-        "adapters": adapters.h01_materialization_adapter_objects,
-        "bases": None
-    },
-    SCHEMAS.MINNIE65_MATERIALIZATION: {
-        "externals": externals.minnie65_materialization,
-        "adapters": adapters.minnie65_materialization_adapter_objects,
-        "bases": None
-    },
-
-}
+djp.enable_datajoint_flags()
+
+h01_materialization_config = SchemaConfig(
+    module_name='h01_materialization',
+    schema_name='microns_h01_materialization',
+    externals=externals.h01_materialization,
+    adapters=adapters.h01_materialization
+)
+
+minnie65_materialization_config = SchemaConfig(
+    module_name='minnie65_materialization',
+    schema_name='microns_minnie65_materialization',
+    externals=externals.minnie65_materialization,
+    adapters=adapters.minnie65_materialization
+)

python/microns-materialization-api/microns_materialization_api/config/adapters.py

@@ -46,10 +46,10 @@ def get(self, filepath):
 
 # also store in one object for ease of use with virtual modules
 
-h01_materialization_adapter_objects = {
+h01_materialization = {
     'h01_meshes': h01_meshes,
 }
 
-minnie65_materialization_adapter_objects = {
+minnie65_materialization = {
     'minnie65_meshes': minnie65_meshes,
 }

python/microns-materialization-api/microns_materialization_api/config/externals.py

@@ -1,22 +1,19 @@
 """
 Externals for DataJoint tables.
 """
-
+import datajoint.datajoint_plus as djp
 from pathlib import Path
-from microns_utils import config_utils
 
 base_path = Path() / '/mnt' / 'dj-stor01' / 'microns'
 
 #h01 materialization
 h01_materialization_external_meshes_path = base_path / 'h01' / 'meshes'
 h01_materialization = {
-    'h01_meshes': config_utils.make_store_dict(h01_materialization_external_meshes_path),
-
-    }
+    'h01_meshes': djp.make_store_dict(h01_materialization_external_meshes_path),
+}
 
 #minnie65_materialization
 minnie65_materialization_external_meshes_path = base_path / 'minnie' / 'meshes'
 minnie65_materialization = {
-    'minnie65_meshes': config_utils.make_store_dict(minnie65_materialization_external_meshes_path),
-
-    }
+    'minnie65_meshes': djp.make_store_dict(minnie65_materialization_external_meshes_path),
+}

python/microns-materialization-api/microns_materialization_api/schemas/h01_materialization.py

@@ -0,0 +1,15 @@
+"""
+DataJoint tables for importing h01 from Jeff Lichtman group.
+"""
+import datajoint as dj
+import datajoint.datajoint_plus as djp
+
+from ..config import h01_materialization_config
+
+h01_materialization_config.register_externals()
+h01_materialization_config.register_adapters(context=locals())
+
+schema = dj.schema(h01_materialization_config.schema_name, create_schema=True)
+
+schema.spawn_missing_classes()
+schema.connection.dependencies.load()